Abstract
Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5′end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation.
Highlights
DNA mutations are the main known source of heritable phenotypic variation, but epimutations, such as heritable changes of gene expression associated with gain or loss of DNA methylation, are a source of phenotypic variability
We report a case of extensive epigenetic variation in natural populations of the flowering plant Arabidopsis thaliana, which concerns a gene involved in starch metabolism, named Qua-Quine Starch (QQS)
In view of the recent evolutionary origin of QQS, we speculate that genes that emerge from scratch could be prone to epigenetic variation
Summary
DNA mutations are the main known source of heritable phenotypic variation, but epimutations, such as heritable changes of gene expression associated with gain or loss of DNA methylation, are a source of phenotypic variability. Examples of epimutable loci in Arabidopsis thaliana (A. thaliana) include the PAI [7] and ATFOLT1 genes [8], which have suffered siRNA-producing duplication events in some accessions and the well characterized FWA locus, which contains a set of SINE-derived siRNA-producing tandem repeats at its 59end [4,5]. Sporadic gain or loss of DNA methylation associated with changes in gene expression has only been documented in A. thaliana mutation accumulation lines [13,14] and examples of natural epigenetic variation in other plant species are few [15,16,17]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
